RetrogeneDB ID: retro_mmul_1935

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:21644400..21645110(-)
• Located in intron of: ENSMMUG00000009439

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSMMUG00000017760
• Aliases: None
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_mmul_1935
ATGGCTTCTCGGTGGCAGGCTGTAGGGGCCTCTGTGCGCTGGAGATCTCTCCAGCACCAGGAGCAGCTTGAGGACAGCAA
GGAGCTGCAGCCTGTGGCCAGCCATCCAGGAGACCTCTGCCACAGCCCTGGGTTCCCTGTGCAGACAGTTCCAAAGGAGG
CTGCCCCTGACAGCCGTCAACCTCAACCTCTGGGGAGACCCCTCCTGGAAACACCTGGAAACCCCAGAGCCAGGGCAGCA
GAGCCTCCAGGCTGCAGCTCGCTCAGCTAAGAGTGCCTTGGATGCCAAGTACCAGAGAATCCAAGAGTCCTGACACCAAG
TGGCTAGTGGAGACTCAGGTGAAGGCCAGGAGGAGGAAGAGAGGGGCACAGAAGAGCAGTGGATCCCCTCAGGCTCACAG
CCTGAGCCAGAAGAGCACCCAGCTGTCTGGAGGCGCCCCTGCCCACTCAGCCGCAGACCTCTGGGAGAAGGAGCATCACT
GCCTCTCTGCCCGGATGGGTTCACGTACCCACCCACTACGGCAGTTGAGGCAGGAGTCTGCCTTCCAGAGCCCTTACTCC
TTGACAGAGCCCCTCTGCTCTCCCAGCGAGTCTGACAGTGACCTAAAGCCTGTGGAGGCAGAACAGCATCTCCAGAAGCT
GTCCCAAGAGCTGGACGAAGCCATTATGGCAGAAGAGAGTGGTGACATGAGCGTCTCTCTCACTGATGAC

Alignment

ORF - retro_mmul_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.38 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASRWQSMGTSVRRRSLRHQEQLEDSKELQPVASH-QETSAGALGSLCRQFQRRLPLRAVNLNLCTGPSW
          MASRWQ..G.SVR.RSL.HQEQLEDSKELQPVASH.QETSA.ALGSLCRQFQRRLPL.AVNLNL...PSW
Retrocopy MASRWQAVGASVRWRSLQHQEQLEDSKELQPVASH>QETSATALGSLCRQFQRRLPLTAVNLNLWGDPSW

Parental  KRLETPEPGQQGLQAAARSAKSALGAMSQRIQ-ESCQSGTKWLVETHVKARRRKRGAQTGSGSP-AHSLS
          K.LETPEPGQQ.LQAAAR...SA..A.....Q.ES....TKWLVET.VKARRRKRGAQ..SGSP.AHSLS
Retrocopy KHLETPEPGQQSLQAAAR---SAKSALDAKYQ>ESKSPDTKWLVETQVKARRRKRGAQKSSGSPQAHSLS

Parental  QKSTRLSGAAPAHSATEPWEKERHHLSARMGSRAHPSRRSRREAAFRSPYSSTEPLCSPRQSDSDPEPVG
          QKST.LSG.APAHSA...WEKE.H.LSARMGSR.HP.R..R.E.AF.SPYS.TEPLCSP..SDSD..PV.
Retrocopy QKSTQLSGGAPAHSAADLWEKEHHCLSARMGSRTHPLRQLRQESAFQSPYSLTEPLCSPSESDSDLKPVE

Parental  AGIQHLQKLSQELEEAIMAXXSGDI-ISLIHD
          A..QHLQKLSQEL.EAIMA..SGD...SL..D
Retrocopy AE-QHLQKLSQELDEAIMAEESGDMSVSLTDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.22 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.06 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.12 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1935 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1935 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3030
Pan troglodytes	retro_ptro_2044
Gorilla gorilla	retro_ggor_2091
Pongo abelii	retro_pabe_2509

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935 , retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,